Mirror viewmodel for Source engine, ends up horribly deformed?
It is really hard to keep with the expectations of the Source Engine while in Blender (I do Dota2 workshop stuff, I should know), so this is some stuff that you should check from my similar struggles:


Do the animations play right? Do they look right in blender?
What does the source model viewer show?
Is the scale, location, and rotation applied (correctly)?  
Did you consider that Source is sensitive to bone labels?


Example:  If you simply mirrored the model and animations, Source will still attempt to align bone labeled "right" to the right hand side for IK purposes, and vice-versa for the left hand side.  
If your model looks wrong in the Source Model Viewer, try creating a custom, unused animation.  If that imports correctly, your animations are mirrored incorrectly.  

Are you able to export the model/animations and directly re-import them successfully without modifications?


Failure to do so suggests something wrong with your tooling or process.  



Without more to go on, I can only provide these generic troubleshooting tips.